Learners can use the molecule editor to learn how to create molecules. The
molecule editor allows learners to draw molecules that follow the rules for
covalent bond formation and formal charge, even if the molecules are chemically
impossible, are unstable, or do not exist in living systems. The molecule
editor warns learners if they try to submit a structure that is chemically
impossible.

The molecule editor incorporates two tools: the JSME molecule editor created by
Peter Erl and Bruno Bienfait, and JSmol, a JavaScript-based molecular viewer
from Jmol. (You don’t need to download either of these tools–Studio uses them
automatically.) For more information about the JSME molecule editor, see JSME
Molecule Editor. For more information
about JSmol, see JSmol.

The molecule that appears when the tool starts is a dopamine
molecule. To use a different molecule, download the .mol file for that
molecule from the list of molecules on the BioTopics website. Then, upload the .mol file to the
Files & Uploads page for your course in Studio, and change “dopamine.mol”
in the example code to the name of your .mol file.

To create the molecule editor that appears in the image above, you need an HTML
component followed by a problem component.

Upload all of the files listed above to the Files & Uploads page in your
course.

Create the HTML component.

In the unit where you want to create the problem, click HTML under
Add New Component, and then click HTML.

In the component that appears, click Edit.

In the component editor, paste the HTML component code from below.

Make any changes that you want, and then click Save.

Create the problem component.

Under the HTML component, click Problem under Add New Component,
and then click Blank Advanced Problem.

<h3>Molecule Editor</h3><p>The molecule editor makes creating and visualizing molecules easy. A chemistry professor may have you build and submit a molecule as part of an exercise.</p><div><scripttype="text/javascript">// <![CDATA[function toggle2(showHideDiv, switchTextDiv) { var ele = document.getElementById(showHideDiv); var text = document.getElementById(switchTextDiv); if(ele.style.display == "block") { ele.style.display = "none"; text.innerHTML = "+ open"; } else { ele.style.display = "block"; text.innerHTML = "- close"; } }// ]]></script></div><div><styletype="text/css"></style></div><divid="headerDiv"><divid="titleText">Using the Molecule Editor<aid="myHeader"href="javascript:toggle2('myContent','myHeader');">+ open </a></div></div><divid="contentDiv"><divid="myContent"style="display: none;"><p>In this problem you will edit a molecule using the molecular drawing program shown below:</p><imgalt=""src="/static/MoleculeEditor_HTML.png"/></div></div><p>&nbsp;</p><divid="headerDiv"><divid="titleText">Are the molecules I've drawn chemically possible?<aid="IntroductionHeader"href="javascript:toggle2('IntroductionContent','IntroductionHeader');">+ open </a></div></div><divid="contentDiv"><divid="IntroductionContent"style="display: none;"><p>The chemical editor you are using ensures that the structures you draw are correct in one very narrow sense, that they follow the rules for covalent bond formation and formal charge. However, there are many structures that follow these rules that are chemically impossible, unstable, do not exist in living systems, or are beyond the scope of this course. The editor will let you draw them because, in contrast to the rules of formal charge, these properties cannot be easily and reliably predicted from structures.</p><p>If you submit a structure that includes atoms that are not possible or are beyond the scope of this course, the software will warn you specifically about these parts of your structure and you will be allowed to edit your structure and re-submit. Submitting an improper structure will not count as one of your tries. In general, you should try to use only the atoms most commonly cited in this course: C, H, N, O, P, and S. If you want to learn about formal charge, you can play around with other atoms and unusual configurations and look at the structures that result.</p></div></div><divid="ap_listener_added">&nbsp;</div>